Recalibrated DNA clock suggests we can stop looking for early primate fossils

The molecular evolution of primates is remodeled based on body and brain size …

The earliest primate fossils unearthed thus far are only 56 million years old, but molecular estimates of the rate of primate evolution predict that there should be some dating back to the Late Cretaceous, closer to 82 million years ago. This is embarrassing for scientists, akin to the time in 1929 when Edwin Hubble measured the age of the Universe as less than half the age of the Earth.

One possible explanation is that earlier fossils are out there, but that no one has found them yet. But Michael Steiper and Erik Seiffert have proposed an alternate reconciliation in a new study of the molecular rate of evolution. Their work was published in the Proceedings of the National Academy of Sciences.

Primate molecular evolution is thought to be related to the size of the animals’ bodies and brains; in contrast to other features, these are easily measurable even in fossils. (Brain size is measured as endocranial volume.) Steiper and Seiffert measured these traits in both living primates and in fossils of extinct primates. They then examined how these traits correlated with molecular rates of evolution using DNA databases of the living primates. Finally, they used their new-found correlation to predict the evolutionary rate of extinct primates based on the sizes of the fossils.

Traditionally, fossils have been used only as calibrations when generating molecular rates—they give us times for when certain species diverged, for example. This method of generating a rate estimate is a significant departure.

The authors found that primates have gotten larger over time; our last common ancestor was quite small, similar in size to a mouse lemur. Moreover, size is inversely proportional to molecular rates of evolution, so as primates have gotten larger, our evolution has slowed down. Extinct primates thus evolved more quickly than had previously been thought, accounting for the fact that they show up later in the fossil record than molecular estimates indicated they should. The new, "corrected" molecular clock generated here puts the earliest primates between 63 and 70 million years ago, closer to where the fossils have been found.

Why should body size and rates of DNA change be related? There are two hypotheses. One is that these mutations vary directly with generation time: shorter generations mean more generations in a given length of time and thus more chances to accrue mutations. The other is that mutations vary inversely with body size because smaller animals have higher metabolic rates and therefore generate more DNA-damaging free radicals.

Since larger-brained animals tend to live longer, the finding that evolutionary rates slow as brain size grows is consistent with the idea that DNA mutations are generated primarily during the turnover of generations. But large-brained primates have high metabolic rates for their size, which doesn't square with the body-size hypothesis.

There are similar discrepancies between molecular and fossil timescales of other mammals; the authors suggest that perhaps this method can be used to reconcile them as well.

56 Reader Comments

The earliest primate fossils unearthed thus far are only 56 million years old, but molecular estimates of the rate of primate evolution predict that there should be some dating back to the Late Cretaceous, closer to 82 million years ago. This is embarrassing for scientists, akin to the time in 1929 when Edwin Hubble measured the age of the Universe as less than half the age of the Earth.

I would agree with longevity affecting rates of evolution. Brain size variations seems something to look into but seems off base to make a theory or make conclusions about. More likely correlation, more information needed.

"Why should body size and rates of DNA change be related? There are two hypotheses. One is that these mutations vary directly with generation time: shorter generations mean more generations in a given length of time and thus more chances to accrue mutations. The other is that mutations vary inversely with body size because smaller animals have higher metabolic rates and therefore generate more DNA-damaging free radicals."

Isn't the latter hypothesis almost Lamarckianism? I'm not sure how intra-lifetime DNA mutations from free radicals are being proposed to affect the next generation, unless the damage is to the sperm or ovum themselves.

Isn't the latter hypothesis almost Lamarckianism? I'm not sure how intra-lifetime DNA mutations from free radicals are being proposed to affect the next generation, unless the damage is to the sperm or ovum themselves.

Isn't this exactly what happens? Hence the Autism study relating rates to age of parents.

The earliest primate fossils unearthed thus far are only 56 million years old, but molecular estimates of the rate of primate evolution predict that there should be some dating back to the Late Cretaceous, closer to 82 million years ago. This is embarrassing for scientists, akin to the time in 1929 when Edwin Hubble measured the age of the Universe as less than half the age of the Earth.

i don't see how those are even vaguely comparable.

Yeah, I'm not seeing how not finding fossils yet is embarassing. Finding fossils is largely a matter of luck (although very skilled, archaeologists and paleontologists are very dependent on the right circumstances to find fossils - hence my saying its largely luck).

Isn't the latter hypothesis almost Lamarckianism? I'm not sure how intra-lifetime DNA mutations from free radicals are being proposed to affect the next generation, unless the damage is to the sperm or ovum themselves.

Germ cells are no exception. They have metabolism and they accumulate DNA errors.

Isn't the latter hypothesis almost Lamarckianism? I'm not sure how intra-lifetime DNA mutations from free radicals are being proposed to affect the next generation, unless the damage is to the sperm or ovum themselves.

Well at least sperm cells are constantly produced. And the production process could accumulate damage over time, and so introduce errors in the sperm.

Isn't it possible that smaller animals tend to evolve faster because it's more beneficial for them to evolve faster, given their need to find novel ways to protect against predators, adapt to close-by food sources, etc., and that the rate of DNA change is itself selectable? I mean, creatures have all sorts of mechanisms to eliminate errors in replication-- mechanisms that themselves can be selected as being more or less effective. Thus the size-to-DNA-change is just a correlation not a cause...

I'm not sure how robust an effect it would have, but wouldn't larger intracranial volume (hopefully) correlate with increases in intelligence and problem solving? If this is the case, then couldn't it be argued that as a species becomes more intelligent, it has a greater capacity to mitigate evolutionary pressures, slowing down evolution.

A classic example is modern medicine -- as we get better at medicine, we allow certain traits to remain in the gene pool which would have otherwise been removed through natural selection.

Isn't it possible that smaller animals tend to evolve faster because it's more beneficial for them to evolve faster, given their need to find novel ways to protect against predators, adapt to close-by food sources, etc., and that the rate of DNA change is itself selectable? I mean, creatures have all sorts of mechanisms to eliminate errors in replication-- mechanisms that themselves can be selected as being more or less effective. Thus the size-to-DNA-change is just a correlation not a cause...

That's kind of what I was thinking. I get the idea of genetic mutations for the sake of mutation, but in terms of adaptation I'm not sure random mutations are what you would be seeing. I mean for smaller animals lower in the food chain there is going to be much more external pressure in order to stay alive. Once you being to reach the top of the food chain those external pressures decrease and at that point adaptation pressure comes only from your environment.

Isn't it possible that smaller animals tend to evolve faster because it's more beneficial for them to evolve faster, given their need to find novel ways to protect against predators, adapt to close-by food sources, etc., and that the rate of DNA change is itself selectable? I mean, creatures have all sorts of mechanisms to eliminate errors in replication-- mechanisms that themselves can be selected as being more or less effective. Thus the size-to-DNA-change is just a correlation not a cause...

That's kind of what I was thinking. I get the idea of genetic mutations for the sake of mutation, but in terms of adaptation I'm not sure random mutations are what you would be seeing. I mean for smaller animals lower in the food chain there is going to be much more external pressure in order to stay alive. Once you being to reach the top of the food chain those external pressures decrease and at that point adaptation pressure comes only from your environment.

A higher predation rate doesn't induce mutation, but it can accentuate it. Particularly in a case where a mutation makes an animal more likely to stay alive (camouflage, body structure change that improves agility or speed, etc), that survival translates to a mutation being spread further. A large primate with low birth rates and less predation pressure doesn't necessarily have fewer mutations, it's just less likely for mutations to be pushed into dominance because survival by means other than mutation have already been achieved.

This didn't really fit into the story, but there's a bit of validation of the general drift in a second paper that came out this week, this time looking at frogs:http://mbe.oxfordjournals.org/content/e ... bev.mss069"Fast Molecular Evolution Associated with High Active Metabolic Rates in Poison Frogs".

Another possible mechanism for an increased rate of evolution is a higher number of available ecological niches, I think. The removal of dinosaurs allowed an explosion in the evolution of mammals and new mammal species, I think, due to reduced "resistance" from pre-existing occupants of those vacated niches. Mammals rapidly evolved (relatively) to fill the vacated niches.New environmental factors (extinctions) may (again, my supposition) allow for an increased rate of development of new species, at least. The governing force being less selective pressure working against these new species as they "find" (move into) the newly available niches and more "successful" mutations. Of course, I could be full of it depending on how they define evolution, precisely, in this case of primates. If they're only looking at mutation rates and not "successful" mutation rates I'm definitely wrong. Though how you'd distinguish at this time frame I'm not sure.Just thinking.

The idea that a molecular DNA clock can measure evolutionary time is just an heuristic. It presumably does have some value. But, it is almost certanly a gross oversimplfication that can't really be relied on for much of anything.

Isn't the latter hypothesis almost Lamarckianism? I'm not sure how intra-lifetime DNA mutations from free radicals are being proposed to affect the next generation, unless the damage is to the sperm or ovum themselves.

Isn't this exactly what happens? Hence the Autism study relating rates to age of parents.

I think the proposed autism mechanism is epigenetic, so it wouldn't affect the germ line, although it's been known for a while now that epigenetic effects can be passed on to future generations (e.g. the finding that grandchildren of Dutch women who were malnourished during WWII are smaller than grandchildren of Dutch women who weren't malnourished).

Isn't the latter hypothesis almost Lamarckianism? I'm not sure how intra-lifetime DNA mutations from free radicals are being proposed to affect the next generation, unless the damage is to the sperm or ovum themselves.

Isn't this exactly what happens? Hence the Autism study relating rates to age of parents.

I think the proposed autism mechanism is epigenetic, so it wouldn't affect the germ line, although it's been known for a while now that epigenetic effects can be passed on to future generations (e.g. the finding that grandchildren of Dutch women who were malnourished during WWII are smaller than grandchildren of Dutch women who weren't malnourished).

I know there was a new study released recently that, according to the headline, said multiple genes were found to be involved in autism. I didn't actually read the study; was it saying they were affected epigenetically? Sincere question.

Has it been proven that genetic drift is relatively constant over time? And is it accepted that genetic drift is a random process related to free radicals or cosmic rays, etc. and that DNA doesn't mutate or drift due directly to an environmental stressor? Is it the environmental stressor that determines which randomly induced DNA change will be beneficial to the animal, thus indirectly determining genetic drift? I am a bit fuzzy on that part of the science.

It seems to me that if my understanding is correct that DNA damage/mutations rates would be hard to measure or predict as there are many factors contributing. Cosmic rays haven't always been constant, free radicals being present in the organism has many contributing factors as to what would govern the rate of them being generated or being present, metabolism is mentioned, but what about diet, environmental stress, social stress, health, etc. Am I wrong or does it seem like an immature leap (as in lack of backup science) that is trying to be pulled off with this theory?

Isn't the latter hypothesis almost Lamarckianism? I'm not sure how intra-lifetime DNA mutations from free radicals are being proposed to affect the next generation, unless the damage is to the sperm or ovum themselves.

Isn't this exactly what happens? Hence the Autism study relating rates to age of parents.

I think the proposed autism mechanism is epigenetic, so it wouldn't affect the germ line, although it's been known for a while now that epigenetic effects can be passed on to future generations (e.g. the finding that grandchildren of Dutch women who were malnourished during WWII are smaller than grandchildren of Dutch women who weren't malnourished).

I know there was a new study released recently that, according to the headline, said multiple genes were found to be involved in autism. I didn't actually read the study; was it saying they were affected epigenetically? Sincere question.

Actually I'm having a total brain fade, AFAIK the studies (there were three) all did exome sequencing, so they wouldn't have detected any epigenetic modifications.

The idea that a molecular DNA clock can measure evolutionary time is just an heuristic. It presumably does have some value. But, it is almost certanly a gross oversimplfication that can't really be relied on for much of anything.

Has it been proven that genetic drift is relatively constant over time? And is it accepted that genetic drift is a random process related to free radicals or cosmic rays, etc. and that DNA doesn't mutate or drift due directly to an environmental stressor? Is it the environmental stressor that determines which randomly induced DNA change will be beneficial to the animal, thus indirectly determining genetic drift? I am a bit fuzzy on that part of the science.

Properly calibrated molecular clocks (a relevant outgroup, solid dates on a few divergences via fossils) do seem to be accurate. But these seem to work best within fairly narrow lineages - so, for example, an "all mammal" or even (as seen here) an "all primate" clock is a bit too broad, and gets species with radically different reproduction rates and lifestyles that throws things off.

Presumably, things like environmental stressors average out over millions of years, unless some species is living in a cave with high uranium content or something.

The molecular clock stuff isn't immature at this point - people were trying it even before i was in grad school, which is a Very Long Time Ago now. You have to be cautious about how you use it, especially if it's the only timing information you have, but most of the reasons to be cautious are pretty well understood.

And of course it is crucial for diversification theories if some groups go boom after the KPg mass extinction.

But thanks, I had missed the point that the molecular clock used was based on trait change rates. There is a lot of argued clocks around that tries to permit rate changes and hence gets from many times wrong worst case down to these tens of percents (if that). Oh, and probably what Dr Jay said on width of lineages. These clocks remind me of the similar problem to allow horizontal gene transfer, which when fixed recovers nice tree phylogenies as opposed to the immediate impression of chaos.

But a poor astrobiology student can't take time to dig into all of these.

dnjake wrote:

The idea that a molecular DNA clock can measure evolutionary time is just an heuristic. It presumably does have some value. But, it is almost certanly a gross oversimplfication that can't really be relied on for much of anything.

No, some of it is theory based what I know. Near neutral drift theory predicts that some changes happens at narrowly distributed times. It is precisely as a radioactive clock in that way. The problem is, besides good calibration (lineage splits doesn't allow for that, even less splits estimated from spurious fossils), that the distributions vary over time in unknown ways.

Some of it is heuristic, I think it has been observed in some cases that instead selection fixes traits at a homogeneous rate. That may depend on a lot of things. The idea to look at trait morphological change rates may come in between.

And of course it is crucial for diversification theories if some groups go boom after the KPg mass extinction.

But thanks, I had missed the point that the molecular clock used was based on trait change rates. There is a lot of argued clocks around that tries to permit rate changes and hence gets from many times wrong worst case down to these tens of percents (if that). Oh, and probably what Dr Jay said on width of lineages. These clocks remind me of the similar problem to allow horizontal gene transfer, which when fixed recovers nice tree phylogenies as opposed to the immediate impression of chaos.

But a poor astrobiology student can't take time to dig into all of these.

dnjake wrote:

The idea that a molecular DNA clock can measure evolutionary time is just an heuristic. It presumably does have some value. But, it is almost certanly a gross oversimplfication that can't really be relied on for much of anything.

No, some of it is theory based what I know. Near neutral drift theory predicts that some changes happens at narrowly distributed times. It is precisely as a radioactive clock in that way.

Some of it is heuristic, I think it has been observed in some cases that instead selection fixes traits at a homogeneous rate. That may depend on a lot of things. The idea to look at trait morphological change rates may come in between.

Maxipad wrote:

Someone's trying to start a fight here.

Or simply bring in the clowns during potty break.

If I understand you correctly, wouldn't selection fix traits at a rate that was related to the rate of environmental change? Under most circumstances the rate of trait fixing/change is uniform (homogeneous) but under extraordinary circumstances (mass extinction events, etc.), rapid rate of fixing/change?Or am I missing something?

I know that the degree of fixation (i.e. alleles that gets to a stable ratio) due to selection depends on population sizes, that is why humans is believed to evolve at an arguably unprecedented rate. Drift, random fixation say if an allele crowds out all others by pure luck, isn't sensitive to that, in theory.

But then you have effects like the initial supply of variation in alleles. If your alleles appears slower than selection may fixate them, they should set the rate.

During bottlenecks alleles are mainly fixed by drift (random fixation), I think. Here it is more by pure luck who survives instead of who crowds out who in larger populations.*

If you have enough variation initially and meanwhile (mutation rate), a large enough population (avoids randomness effects which in more severe in low populations or conversely picks up smaller differences in fitness) and a slowly enough changing environment, ideally selection _should_ set the rate, or in other words some relation to the environment as you say.

---------------It's sort of the same yin-yang that positive vs negative selection offers. Wonder if biologists call it "positive" and "negative" drift? =D

Cue the IDiots claiming "see, SEE, this DISPROVES the theory of evolution!!1!1!!!!".

Oh, and goddidit.

You're going to need to try harder than that. The Bible mentions 4 races: seraphim, nephilim, cherubim, and mankind. The opening of the Bible says, "Let US make man in OUR image."

Apes evolved on Earth. Something altered them in a way that left a missing link in fossil records.

Evolution and Creation can coexist.

The length of a day to God, in the absence of the Sun until the 4th day, must be so totally different than what we consider a day on Earth. Even then, the length of a day is not constant, as it keeps becoming longer and longer due to the moon; so, it is evident that preachers introduced a lot of inaccuracies and confusion brought about by translation literalism.

I know that the degree of fixation (i.e. alleles that gets to a stable ratio) due to selection depends on population sizes, that is why humans is believed to evolve at an arguably unprecedented rate. Drift, random fixation say if an allele crowds out all others by pure luck, isn't sensitive to that, in theory.

But then you have effects like the initial supply of variation in alleles. If your alleles appears slower than selection may fixate them, they should set the rate.

During bottlenecks alleles are mainly fixed by drift (random fixation), I think. Here it is more by pure luck which survives instead of who crowds out who in larger populations.*

If you have enough variation initially and meanwhile (mutation rate), a decent population and a slowly enough changing environment, ideally selection _should_ set the rate, or in other words some relation to the environment as you say.

---------------It's sort of the same yin-yang that positive vs negative selection offers. Wonder if biologists call it "positive" and "negative" drift? =D

Apes evolved on Earth. Something altered them in a way that left a missing link in fossil records.

Predictably, in comes the clowns/trolls/poes. Despite that people should "try harder" and all.

A remaining link, a transitional fossil, is by definition not missing. All apes vary by degree, and no biologist would claim a transitional fossil that only exists between groups. (Think of the epinymous transitional fossils between artiodactyls and cetaceans.)

Vapur9 wrote:

Evolution and Creation can coexist.

BS. The scientific theory is founded on facts and permits no "unseen" agency. The religious idea is founded on making shit up and is based on "unseen" agency. You have to choose between evolution science, its theory based on its facts, and creationist religion, its ideas based on its stated texts.

The scientific theory is founded on facts and permits no "unseen" agency. The religious idea is founded on making shit up and is based on "unseen" agency. You have to choose between evolution science, its theory based on its facts, and creationist religion, its ideas based on its stated texts.

The Big Bang is an unseen agency, whose background noise can be measured and postulated to have been in another form. There is nothing "factual" about it except that, as a theory, it could turn out to be correct. That's faith from a scientific standpoint, that we evolved from it.

I, personally, think the 6000 year-old Earth idea is ridiculous; however, I recognize that whatever created us, this Universe, is also capable of creating personalities, something unseen. Who is to say that it itself doesn't have one?